Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015222.1 Kokia drynarioides strain JFW-HI SEQ_130266, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 288427
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 409 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--38 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39 GCAACGCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4003 original size:64 final size:63
Alignment explanation
Indices: 3902--4024 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 63
3892 TGTATATATA
* * * *
3902 ATATATAATTTATTAATAAACTAAAAATTTGACTATAAATATATGCGTG-AAAATATTTAATTGT
1 ATATATAATTTATCAACAAACTAAAAATATGACTATAAAGATAT--GTGAAAAATATTTAATTGT
* *
3966 ATATATGATTTATCAACAAACTAAAAAGTAT-ATTATAAAGATATGTGAAAAATATTTAA
1 ATATATAATTTATCAACAAACTAAAAA-TATGACTATAAAGATATGTGAAAAATATTTAA
4025 AAACATCGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 3 0.06
63 11 0.22
64 35 0.69
65 2 0.04
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (63 bp):
ATATATAATTTATCAACAAACTAAAAATATGACTATAAAGATATGTGAAAAATATTTAATTGT
Found at i:8268 original size:18 final size:16
Alignment explanation
Indices: 8237--8274 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
8227 TTATTTGGAC
8237 TTTACATTTATTTTAT
1 TTTACATTTATTTTAT
8253 TTTACCATTGTATTTTAT
1 TTTA-CATT-TATTTTAT
8271 TTTA
1 TTTA
8275 ACAAAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 4 0.20
18 12 0.60
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTACATTTATTTTAT
Found at i:8338 original size:17 final size:17
Alignment explanation
Indices: 8316--8354 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
8306 CTCTACCTTG
* * *
8316 ACAAGAATTCTCTATGA
1 ACAAGAACTCTCAACGA
8333 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
8350 ACAAG
1 ACAAG
8355 TTCTCCAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:12932 original size:30 final size:29
Alignment explanation
Indices: 12898--12972 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
12888 CATTTAACAC
12898 AACAGTCACTCAACT-TTGAAAATGTGACAA
1 AACAGTCACT-AACTATTGAAAA-GTGACAA
*
12928 AACAGTCATTAACGTTATTGAAAAGTGACAA
1 AACAGTCACTAAC--TATTGAAAAGTGACAA
*
12959 AATAGTCACTAACT
1 AACAGTCACTAACT
12973 CAACCCTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 4 0.10
30 9 0.23
31 19 0.49
32 7 0.18
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (29 bp):
AACAGTCACTAACTATTGAAAAGTGACAA
Found at i:19365 original size:20 final size:18
Alignment explanation
Indices: 19337--19379 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
19327 TTTTAATTAT
19337 TAAAATTACTAATAATAAAA
1 TAAAATTAC-AA-AATAAAA
*
19357 TAAACTTACAAAATAAAA
1 TAAAATTACAAAATAAAA
19375 -AAAAT
1 TAAAAT
19380 AAAACAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 2 0.10
20 8 0.38
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAATTACAAAATAAAA
Found at i:22106 original size:20 final size:20
Alignment explanation
Indices: 22081--22118 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22071 TATTTTATTT
22081 TATTTATAGTATATTATTAC
1 TATTTATAGTATATTATTAC
* *
22101 TATTTATATTTTATTATT
1 TATTTATAGTATATTATT
22119 TAACTGAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TATTTATAGTATATTATTAC
Found at i:22120 original size:14 final size:14
Alignment explanation
Indices: 22070--22120 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
22060 TTATTATTGT
22070 TTATTT-TATTTTA
1 TTATTTATATTTTA
*
22083 TTTATAGTATATTATTA
1 -TTAT-TTATATT-TTA
*
22100 CTATTTATATTTTA
1 TTATTTATATTTTA
22114 TTATTTA
1 TTATTTA
22121 ACTGAGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 13 0.43
15 7 0.23
16 7 0.23
17 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTTATATTTTA
Found at i:31215 original size:15 final size:17
Alignment explanation
Indices: 31173--31215 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
31163 TTTTAAGACA
31173 ATAATTATATATGTATAT
1 ATAATTA-ATATGTATAT
*
31191 ATAATAAATATGTATA-
1 ATAATTAATATGTATAT
31207 A-AATTAATA
1 ATAATTAATA
31216 ATTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 9 0.39
18 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
ATAATTAATATGTATAT
Found at i:36426 original size:243 final size:247
Alignment explanation
Indices: 35977--36553 Score: 829
Period size: 247 Copynumber: 2.3 Consensus size: 247
35967 ATAATTTTGT
* * *
35977 CTCCCAAAATGATAGATTTATTATTTAGTCCCTTAAAATTTAACGATATTATATATTAATATAAT
1 CTCCCAAAATGATAGATTTATTATTTAATCCCTTAAAATTTAATGATATTATATATTAGTATAAT
** * *
36042 GATAAATTGCACTTCGTCCTAAAAAAAAAAAGAATTGCTGATGTTGAGATACTATAAATTAATTT
66 GATAAATTGCACTTCACCCT--AAAAAAAAAGAATTACTGATGTTAAGATACTAT-AA-TAATTT
* *
36107 ATTAAATTTCAAGTCTTAAATAGAAGGTTGTATAAATCAATAGGGGTAATTACAGATTTAGTTCT
127 ATTAAATTTCAAGTCTTAAACAGAAGGTTGTATAAATCAATAGGGGTAATGACAGATTTAGTTCT
*
36172 TAAAGTTTACATATTTCATGAATTTGATTATTAA-ATTTTTAAAGCTAAATTTGAC
192 TAAAGTTTACATATTTCATCAATTTGATTATTAACATTTTTAAAGCTAAATTTGAC
36227 CTCCCAAAATGATAGATTTATTATTTAATCCCTTAAAATTTAATGATATTATATATTAGTATAAT
1 CTCCCAAAATGATAGATTTATTATTTAATCCCTTAAAATTTAATGATATTATATATTAGTATAAT
* *
36292 GATAAATTGCACTTCACCCT-AAGAGAAAGAATTACTGATGTTAAGATACTAT-A-AATTTATTA
66 GATAAATTGCACTTCACCCTAAAAAAAAAGAATTACTGATGTTAAGATACTATAATAATTTATTA
* *
36354 ATTTTCAAGTCTTAAACAGAAGGTTGTATAAATCAATAGGGGTAATGATAGATTTAGTTCTTAAA
131 AATTTCAAGTCTTAAACAGAAGGTTGTATAAATCAATAGGGGTAATGACAGATTTAGTTCTTAAA
** * * *
36419 GTTTACATATTTTGTCAATTTGATTATTAATCTCTTTTTTTAAGTTAAATTTGAC
196 GTTTACATATTTCATCAATTTGATTATTAA---CATTTTTAAAGCTAAATTTGAC
* * * * * *
36474 CTTCCAAATTGGTAAATTTTTTATTTAATCCCTTAAATTTTAATGATATTATATATTAGTATAAT
1 CTCCCAAAATGATAGATTTATTATTTAATCCCTTAAAATTTAATGATATTATATATTAGTATAAT
*
36539 GATAAATTACACTTC
66 GATAAATTGCACTTC
36554 TACGACAAAT
Statistics
Matches: 297, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
243 97 0.33
245 1 0.00
247 119 0.40
250 80 0.27
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (247 bp):
CTCCCAAAATGATAGATTTATTATTTAATCCCTTAAAATTTAATGATATTATATATTAGTATAAT
GATAAATTGCACTTCACCCTAAAAAAAAAGAATTACTGATGTTAAGATACTATAATAATTTATTA
AATTTCAAGTCTTAAACAGAAGGTTGTATAAATCAATAGGGGTAATGACAGATTTAGTTCTTAAA
GTTTACATATTTCATCAATTTGATTATTAACATTTTTAAAGCTAAATTTGAC
Found at i:44612 original size:2 final size:2
Alignment explanation
Indices: 44605--44637 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44595 TTTAAAAATT
44605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44638 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44948 original size:24 final size:24
Alignment explanation
Indices: 44921--44976 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
44911 AAAGTGGACT
*
44921 TTTAATGCCGGCCATTGATCGGGG
1 TTTAATGCCGACCATTGATCGGGG
* * *
44945 TTTAATGCCGATCATTGATTGGGT
1 TTTAATGCCGACCATTGATCGGGG
44969 TTTAATGC
1 TTTAATGC
44977 AGGACTTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.38
Consensus pattern (24 bp):
TTTAATGCCGACCATTGATCGGGG
Found at i:45576 original size:58 final size:56
Alignment explanation
Indices: 45514--45623 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
45504 TCAAACACTC
* *
45514 AAAAATTATTTTTTTATTCGTATTTTTTGGTATCGACCATTAACTGCCAAACATAAAG
1 AAAAAATAGTTTTTTATT--TATTTTTTGGTATCGACCATTAACTGCCAAACATAAAG
* * * * *
45572 AAAAAATAGTTTTTTATTTTTTTTTTTGTGTCGACCATTAAGTGGCAAACAT
1 AAAAAATAGTTTTTTATTTATTTTTTGGTATCGACCATTAACTGCCAAACAT
45624 CCAAAATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 29 0.64
58 16 0.36
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (56 bp):
AAAAAATAGTTTTTTATTTATTTTTTGGTATCGACCATTAACTGCCAAACATAAAG
Found at i:59906 original size:15 final size:15
Alignment explanation
Indices: 59877--59945 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
59867 CAAAACGTAC
59877 TAATAAATATCATTAA
1 TAAT-AATATCATTAA
* *
59893 TAATAATATTATTAT
1 TAATAATATCATTAA
* * *
59908 TAATAGTAACAGTAA
1 TAATAATATCATTAA
* *
59923 TAATGAGT-TTATTAA
1 TAAT-AATATCATTAA
59938 TAATAATA
1 TAATAATA
59946 AATAAATATT
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
14 2 0.05
15 31 0.77
16 7 0.17
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.41
Consensus pattern (15 bp):
TAATAATATCATTAA
Found at i:59968 original size:20 final size:21
Alignment explanation
Indices: 59934--59973 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
59924 AATGAGTTTA
59934 TTAATAATAATAAATAAATAT
1 TTAATAATAATAAATAAATAT
*
59955 TTAATATTAA-AAATAAATA
1 TTAATAATAATAAATAAATA
59974 AAAAAGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAATAATAATAAATAAATAT
Found at i:61024 original size:30 final size:29
Alignment explanation
Indices: 60971--61058 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
60961 AGAGGTCCCT
*
60971 AAACTGTCCAAAAATCACA-TTTTAACCTC
1 AAACT-TCCAAAAATTACATTTTTAACCTC
* ** *
61000 AAAACTTCTAAAAATTATGTTTTTACCCTC
1 -AAACTTCCAAAAATTACATTTTTAACCTC
* *
61030 GAACTTCCAAAAATTCCATTTTTAACCTC
1 AAACTTCCAAAAATTACATTTTTAACCTC
61059 GATTTTTCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 32 0.70
30 14 0.30
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTAACCTC
Found at i:61069 original size:29 final size:31
Alignment explanation
Indices: 61037--61198 Score: 96
Period size: 30 Copynumber: 5.5 Consensus size: 31
61027 CTCGAACTTC
61037 CAAAAATT-CCATTTTTAACCTCGA-TTTTT
1 CAAAAATTACCATTTTTAACCTCGAGTTTTT
* * * *
61066 CAAAAAATTACCA--TTT-ACCCCGAGATCTC
1 C-AAAAATTACCATTTTTAACCTCGAGTTTTT
* *
61095 CAAAAACTTA--ATTTTTGACCGT-GATTTTTT
1 CAAAAA-TTACCATTTTTAACC-TCGAGTTTTT
* * * *
61125 CAAAAATTACCA-TTTTACCCCCGA--ATGT
1 CAAAAATTACCATTTTTAACCTCGAGTTTTT
* *
61153 CTAAAATT-CCATTTTTGACCTCGAGTTTTT
1 CAAAAATTACCATTTTTAACCTCGAGTTTTT
*
61183 CCAAAATTACCATTTT
1 CAAAAATTACCATTTT
61199 GCCCTCAAGT
Statistics
Matches: 97, Mismatches: 21, Indels: 28
0.66 0.14 0.19
Matches are distributed among these distances:
27 4 0.04
28 29 0.30
29 16 0.16
30 37 0.38
31 11 0.11
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (31 bp):
CAAAAATTACCATTTTTAACCTCGAGTTTTT
Found at i:61160 original size:28 final size:28
Alignment explanation
Indices: 61127--61232 Score: 92
Period size: 28 Copynumber: 3.7 Consensus size: 28
61117 GATTTTTTCA
*
61127 AAAATTACCATTTTACCCCCGAATGTCT
1 AAAATTACCATTTTACCCCCGAATGTCC
* * *
61155 AAAATT-CCATTTTTGA-CCTCGAGTTTTTCC
1 AAAATTACCA-TTTT-ACCCCCGA--ATGTCC
* *
61185 AAAATTACCATTTTGCCCTC-AAGTGTCC
1 AAAATTACCATTTTACCCCCGAA-TGTCC
61213 AAAATTACCATTTTACCCCC
1 AAAATTACCATTTTACCCCC
61233 TGGGTACCCA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
27 3 0.05
28 37 0.60
29 2 0.03
30 17 0.27
31 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAATGTCC
Found at i:61182 original size:59 final size:57
Alignment explanation
Indices: 61020--61226 Score: 192
Period size: 58 Copynumber: 3.5 Consensus size: 57
61010 AAAATTATGT
* *
61020 TTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAACCTCGATTTTTCAAAAAATTACCA
1 TTTTACCCCCGAA-TGT-CAAAAATTCCATTTTTGACCTCGATTTTTC-AAAAATTACCA
* *
61079 -TTTA-CCCCGAGATCTCCAAAAACTT-AATTTTTGACCGT-GATTTTTTCAAAAATTACCA
1 TTTTACCCCCGA-ATGT-CAAAAA-TTCCATTTTTGACC-TCGA-TTTTTCAAAAATTACCA
* *
61137 TTTTACCCCCGAATGTCTAAAATTCCATTTTTGACCTCGAGTTTTTCCAAAATTACCA
1 TTTTACCCCCGAATGTCAAAAATTCCATTTTTGACCTCGA-TTTTTCAAAAATTACCA
* * *
61195 TTTTGCCCTC-AAGTGTCCAAAATTACCATTTT
1 TTTTACCCCCGAA-TGTCAAAAATT-CCATTTT
61227 ACCCCCTGGG
Statistics
Matches: 126, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
57 11 0.09
58 86 0.68
59 23 0.18
60 6 0.05
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (57 bp):
TTTTACCCCCGAATGTCAAAAATTCCATTTTTGACCTCGATTTTTCAAAAATTACCA
Found at i:73664 original size:51 final size:51
Alignment explanation
Indices: 73609--73781 Score: 149
Period size: 51 Copynumber: 3.4 Consensus size: 51
73599 TGACAAGTCT
* * *
73609 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAACATCAATTC
1 TTATCTCTCTGAAGTTGCAGTAAGAGCAAGATAAAGCTTTAACATCAAATC
* ** ** * * *
73660 TTATC-CTCTTGAAGTTGCAATAA-AGTTAGATTAAA--AATAATAGCAAGTC
1 TTATCTCTC-TGAAGTTGCAGTAAGAGCAAGA-TAAAGCTTTAACATCAAATC
* *
73709 TTTATCTCTCTGAAGTCGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATC
1 -TTATCTCTCTGAAGTTGCAGTAAGAGCAAGATAAAGCTTTAACATCAAATC
*
73761 CTATCT-TCCTGAAGTTGCAGT
1 TTATCTCT-CTGAAGTTGCAGT
73782 GAAGTTGGAA
Statistics
Matches: 92, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
49 9 0.10
50 30 0.33
51 45 0.49
52 8 0.09
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (51 bp):
TTATCTCTCTGAAGTTGCAGTAAGAGCAAGATAAAGCTTTAACATCAAATC
Found at i:73787 original size:101 final size:101
Alignment explanation
Indices: 73602--73796 Score: 282
Period size: 101 Copynumber: 1.9 Consensus size: 101
73592 ACTACAATGA
* * * * * *
73602 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAACATCAATTCTTATCCT
1 CAAGTCTTTATCTCTCTGAAGTCGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCT
* *
73667 CTTGAAGTTGCAATAAAGTTAGATTAAAAATAATAG
66 CCTGAAGTTGCAATAAAGTTAGAATAAAAATAATAG
*
73703 CAAGTCTTTATCTCTCTGAAGTCGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCTT
1 CAAGTCTTTATCTCTCTGAAGTCGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCT
* * *
73768 CCTGAAGTTGCAGTGAAGTTGGAATAAAA
66 CCTGAAGTTGCAATAAAGTTAGAATAAAA
73797 CTACAATAGC
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (101 bp):
CAAGTCTTTATCTCTCTGAAGTCGCAGTAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCT
CCTGAAGTTGCAATAAAGTTAGAATAAAAATAATAG
Found at i:74393 original size:209 final size:208
Alignment explanation
Indices: 74027--74678 Score: 807
Period size: 209 Copynumber: 3.1 Consensus size: 208
74017 CACAAATAGC
* *
74027 GATGCAGTCATCTT-TCCGATGAGATACTGAGAAGTA-AACGAAATCAATGAAACAAGGCTCAAA
1 GATGCAGTCATCTTCT-TGATGAGATACTGAGAAGTAGAAC-AAATCAATGAAACAAGGCTCAAT
* *
74090 GCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAAAT
64 GTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAAT
* *
74155 GATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAA
129 GATTAGCTTCCTGATGAGATACCGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
74220 GCAGATTGAAACAAGT
194 GC-GATTGAAACAAGT
* *
74236 GATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGATCAAATCAATGAAACGAGGCTCAATGT
1 GATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGAACAAATCAATGAAACAAGGCTCAATGT
* * * * *
74301 GAGCAAATTTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCAAAGTAATAAAATGG
66 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGA
* * *
74366 TTAGCTTCCTGATGAGATACCGAGAAGTGGATCAAATTCGCCTTCCTGATGAGATA-TGAAGAAG
131 TTAGCTTCCTGATGAGATACCGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAG-AGAAG
74430 CGAATTGAAACAAGT
195 CG-ATTGAAACAAGT
* * ** * * * * * *
74445 GATGCGGTCATCTTCCTGATGAGATACCAAGAAGAAGACCAAATC-A--AACCCACGCTCGATGT
1 GATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGAACAAATCAATGAAACAAGGCTCAATGT
* ** *
74507 GAGCAAATCTTCGAACCTCAGCTTCCTCTTGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGA
66 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGA
* * * * * * *
74572 TTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCCTCTTGATGAAACACAGAGAAGT
131 TTAGCTTCCTGATGAGATACCGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG-
* ** *
74637 GGATCAAAATAAGT
195 CGATTGAAACAAGT
**
74651 GATGTGGTCATCTTC-T-ATGAGATACTGA
1 GATGCAGTCATCTTCTTGATGAGATACTGA
74679 AAAGAATGCC
Statistics
Matches: 385, Mismatches: 52, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
204 10 0.03
205 1 0.00
206 143 0.37
207 2 0.01
208 3 0.01
209 223 0.58
210 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (208 bp):
GATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGAACAAATCAATGAAACAAGGCTCAATGT
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGA
TTAGCTTCCTGATGAGATACCGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
GATTGAAACAAGT
Found at i:75031 original size:6 final size:6
Alignment explanation
Indices: 75020--75085 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
75010 GGCCCAACAG
* * * *
75020 AATTTA AATTT- ATTTTA AGTTTA AATTTA CA-TAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
75065 -ATTATA AATTTA AGTTTA AAT
1 AATT-TA AATTTA AATTTA AAT
75086 CTATTTAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
4 3 0.07
5 8 0.17
6 32 0.70
7 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:75044 original size:17 final size:17
Alignment explanation
Indices: 75020--75082 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 17
75010 GGCCCAACAG
75020 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* ** *
75037 AGTTTAAATTTACATAA
1 AATTTAAATTTATTTTA
*
75054 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
75071 AATTTAAGTTTA
1 AATTTAAATTTA
75083 AATCTATTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:75800 original size:3 final size:3
Alignment explanation
Indices: 75792--75902 Score: 66
Period size: 3 Copynumber: 36.0 Consensus size: 3
75782 TAAATATCAT
* *
75792 TAA TAA TAA TAT TAA TTAA TTAA TAA TAA TAA TAA TAA TAA TAA T-T
1 TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
75838 TAA CAG TAA TAA TGAA T-T TAT TAA TAA TAA TAAA TAAA TATT TAA TAT
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA T-AA TA-A TAA TAA
*
75886 TAA AAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
75903 AAGTTGAAAG
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
2 4 0.05
3 62 0.73
4 19 0.22
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:75847 original size:29 final size:30
Alignment explanation
Indices: 75792--75868 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 30
75782 TAAATATCAT
* *
75792 TAATAATAATATTAA-TTAATTAATAATAA
1 TAATAATAATAATAATTTAATCAATAATAA
*
75821 TAATAATAATAATAATTTAA-CAGTAATAA
1 TAATAATAATAATAATTTAATCAATAATAA
*
75850 TGAATTTATTAATAATAAT
1 T-AA--TAATAATAATAAT
75869 AAATAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 22 0.55
30 6 0.15
32 12 0.30
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (30 bp):
TAATAATAATAATAATTTAATCAATAATAA
Found at i:76949 original size:29 final size:30
Alignment explanation
Indices: 76906--76963 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
76896 GAAAGTCCTT
76906 AAACTATTTAAAAATCACATTTTAACCCCA
1 AAACTATTTAAAAATCACATTTTAACCCCA
* *
76936 AAACT-TTTAAAAATTACATTTTTACCCC
1 AAACTATTTAAAAATCACATTTTAACCCC
76964 CGAACTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.34
Consensus pattern (30 bp):
AAACTATTTAAAAATCACATTTTAACCCCA
Found at i:76969 original size:29 final size:29
Alignment explanation
Indices: 76907--77016 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 29
76897 AAAGTCCTTA
* * **
76907 AACTATTTAAAAATCACATTTTAACCCCAA
1 AACT-TTTAAAAATTACATTTTTACCCCCG
76937 AACTTTTAAAAATTACATTTTTACCCCCG
1 AACTTTTAAAAATTACATTTTTACCCCCG
** * * * *
76966 AACTTCCAAAAAATCCATTTTTAACCTCG
1 AACTTTTAAAAATTACATTTTTACCCCCG
**
76995 ATTTTTTCAAAAATTACCATTT
1 AACTTTT-AAAAATTA-CATTT
77017 AGCCCCGAAT
Statistics
Matches: 62, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
29 47 0.76
30 10 0.16
31 5 0.08
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTTTTAAAAATTACATTTTTACCCCCG
Found at i:77035 original size:58 final size:59
Alignment explanation
Indices: 76915--77076 Score: 136
Period size: 58 Copynumber: 2.7 Consensus size: 59
76905 TAAACTATTT
* *
76915 AAAAATCACA-TTTTAACCCCAAAACTTTT-AAAAATTA-CATTTTTACCCCCGAACTTCCA
1 AAAAATC-CATTTTTAACCCC-GAGCTTTTCAAAAATTACCA-TTTTACCCCCGAACTTCCA
* ** * *
76974 AAAAATCCATTTTTAACCTCGATTTTTTCAAAAATTACCA-TTTAGCCCCGAA-TGTCTA
1 AAAAATCCATTTTTAACCCCGAGCTTTTCAAAAATTACCATTTTACCCCCGAACT-TCCA
* ** * *
77032 AAAATTTTATTTTTGACCCCGAGCTTTTCCAAAATTACCAATTTT
1 AAAAATCCATTTTTAACCCCGAGCTTTTCAAAAATTACC-ATTTT
77077 CCCTCAAGTG
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
57 1 0.01
58 52 0.63
59 25 0.30
60 5 0.06
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAAATCCATTTTTAACCCCGAGCTTTTCAAAAATTACCATTTTACCCCCGAACTTCCA
Found at i:78811 original size:23 final size:22
Alignment explanation
Indices: 78761--78826 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
78751 TAATTTTTTT
* *
78761 AAAATTTTTCTTAATAATAATTC
1 AAAATTTTT-TTAAAAATAATTA
*
78784 TAAATTTTTTTAAAAATATATTA
1 AAAATTTTTTTAAAAATA-ATTA
*
78807 AAAATTATGTTTAAAAATAA
1 AAAATT-TTTTTAAAAATAA
78827 AAAATATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.22
23 17 0.47
24 11 0.31
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATTTTTTTAAAAATAATTA
Found at i:80278 original size:20 final size:20
Alignment explanation
Indices: 80241--80278 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
80231 TTTATATTTA
*
80241 TTTTAAGAATTTTTTTAATT
1 TTTTAAGAATTTTGTTAATT
80261 TTTTAA-AATTGTTGTTAA
1 TTTTAAGAATT-TTGTTAA
80279 GAAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
TTTTAAGAATTTTGTTAATT
Found at i:82575 original size:14 final size:14
Alignment explanation
Indices: 82530--82576 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
82520 ATATAAAAAA
82530 TAAAAAATTAAATT
1 TAAAAAATTAAATT
* **
82544 CTTAAAAA-TAAAAA
1 -TAAAAAATTAAATT
82558 TAAAAAATTAAATT
1 TAAAAAATTAAATT
82572 TAAAA
1 TAAAA
82577 TATACATATA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAAATTAAATT
Found at i:87025 original size:105 final size:105
Alignment explanation
Indices: 86843--87052 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
86833 CAGCAAATAG
*
86843 GTGAAGACTTTGCCTATACCAACACTTAAATCTCAAACTGGTAGAGATGTCTAAAACATGATGCT
1 GTGAAGACTTTGCCTATACCAACACTTAAATCTCAAACTGGTAGAGATGACTAAAACATGATGCT
86908 TTGTGTTTTTACTGCCATTTTTATGGAAAGTGTTTAATGT
66 TTGTGTTTTTACTGCCATTTTTATGGAAAGTGTTTAATGT
*
86948 GTGAAGACTTTGCCTATACCAACACTTAAATCTCAAACTGTTAGAGATGACTAAAACATGATGCT
1 GTGAAGACTTTGCCTATACCAACACTTAAATCTCAAACTGGTAGAGATGACTAAAACATGATGCT
87013 TTGTGTTTTTACTGCCATTTTTATGGAAAGTGTTTAATGT
66 TTGTGTTTTTACTGCCATTTTTATGGAAAGTGTTTAATGT
87053 AGAAAGAACA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (105 bp):
GTGAAGACTTTGCCTATACCAACACTTAAATCTCAAACTGGTAGAGATGACTAAAACATGATGCT
TTGTGTTTTTACTGCCATTTTTATGGAAAGTGTTTAATGT
Found at i:87901 original size:25 final size:25
Alignment explanation
Indices: 87873--87924 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
87863 ATTAGAGACC
87873 ATCTTGAAACAATCCAAAGTCTTGT
1 ATCTTGAAACAATCCAAAGTCTTGT
* *
87898 ATCTTGGAACAGTCCAAAGTCTTGT
1 ATCTTGAAACAATCCAAAGTCTTGT
87923 AT
1 AT
87925 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (25 bp):
ATCTTGAAACAATCCAAAGTCTTGT
Found at i:97605 original size:25 final size:23
Alignment explanation
Indices: 97570--97618 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
97560 TTTATAGTGA
*
97570 TTTGTTTATATTTATATTAATTT
1 TTTGTTTATATTTATACTAATTT
97593 TTTGATTTCATATTTATACTAATTT
1 TTTG-TTT-ATATTTATACTAATTT
97618 T
1 T
97619 GAACTTTACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.17
24 3 0.13
25 16 0.70
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTGTTTATATTTATACTAATTT
Found at i:100456 original size:19 final size:20
Alignment explanation
Indices: 100413--100457 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
100403 AAACATATGG
*
100413 TTTAAAAGAAATAATACGAA
1 TTTAAAAGAAATAATAAGAA
* *
100433 ATTAAAA-AAATAATAATAA
1 TTTAAAAGAAATAATAAGAA
100452 TTTAAA
1 TTTAAA
100458 TTGCGAGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
TTTAAAAGAAATAATAAGAA
Found at i:105603 original size:20 final size:21
Alignment explanation
Indices: 105565--105603 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
105555 TACTATTTCT
*
105565 TTTAAATTTTTGTGTATATTA
1 TTTAAATTTTTGTGGATATTA
105586 TTTAAATTTTT-TGGATAT
1 TTTAAATTTTTGTGGATAT
105604 GAGTATATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTAAATTTTTGTGGATATTA
Found at i:111370 original size:27 final size:26
Alignment explanation
Indices: 111324--111377 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
111314 TTAAATAATA
111324 AAATATAAAATTATATTTAATAATTT
1 AAATATAAAATTATATTTAATAATTT
*
111350 AAATATAAAA-TATCTCATTAATAATTT
1 AAATATAAAATTATAT--TTAATAATTT
111377 A
1 A
111378 GATTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATATAAAATTATATTTAATAATTT
Found at i:132034 original size:16 final size:17
Alignment explanation
Indices: 132008--132041 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
131998 TCAAAATTGG
*
132008 ATTGAAAAAATTATTTA
1 ATTGAAAAAATTAATTA
132025 ATTG-AAAAATTAATTA
1 ATTGAAAAAATTAATTA
132041 A
1 A
132042 AATTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTGAAAAAATTAATTA
Found at i:137332 original size:16 final size:18
Alignment explanation
Indices: 137306--137342 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
137296 TAAAAACCTT
*
137306 AAACTCATAAATCC-TAA
1 AAACTCATAAACCCTTAA
137323 AAAC-CATAAACCCTTAA
1 AAACTCATAAACCCTTAA
137340 AAA
1 AAA
137343 AATCGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (18 bp):
AAACTCATAAACCCTTAA
Found at i:137340 original size:24 final size:24
Alignment explanation
Indices: 137294--137340 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
137284 AAACAAAAAC
* *
137294 CCTAAAAACCTTAAACTCATAAAT
1 CCTAAAAACCATAAACCCATAAAT
*
137318 CCTAAAAACCATAAACCCTTAAA
1 CCTAAAAACCATAAACCCATAAA
137341 AAAATCGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (24 bp):
CCTAAAAACCATAAACCCATAAAT
Found at i:144538 original size:22 final size:23
Alignment explanation
Indices: 144513--144559 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
144503 ATAATTTATT
144513 TTTATAAAAAGT-ATATTTTAAA
1 TTTATAAAAAGTGATATTTTAAA
* * *
144535 TTTATTAAAATTGGTATTTTAAA
1 TTTATAAAAAGTGATATTTTAAA
144558 TT
1 TT
144560 AATTTCATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (23 bp):
TTTATAAAAAGTGATATTTTAAA
Found at i:145475 original size:3 final size:3
Alignment explanation
Indices: 145467--145491 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
145457 AACAATCCTC
145467 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
145492 TTCTTCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:151429 original size:21 final size:22
Alignment explanation
Indices: 151405--151446 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
151395 AACTAAACCC
*
151405 TTTTAAAAAT-TTAAAAATTAT
1 TTTTAAAAATCATAAAAATTAT
151426 TTTTAAAAATCATAAAAATTA
1 TTTTAAAAATCATAAAAATTA
151447 CAAACAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAAATCATAAAAATTAT
Found at i:152245 original size:29 final size:30
Alignment explanation
Indices: 152184--152262 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 30
152174 AATTTTTTAA
* *
152184 TTTAATATTTAATTAAGTATCTGAATTTGT
1 TTTAATATTAAATTAAGTACCTGAATTTGT
**
152214 TTTAATATTAAATTTTGTACCTG-ATTT-T
1 TTTAATATTAAATTAAGTACCTGAATTTGT
** *
152242 TTTTTTATCTCAATTAAGTAC
1 TTTAATAT-TAAATTAAGTAC
152263 TTATATATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 7 0.18
29 13 0.33
30 19 0.49
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (30 bp):
TTTAATATTAAATTAAGTACCTGAATTTGT
Found at i:154919 original size:18 final size:17
Alignment explanation
Indices: 154884--154916 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
154874 GATTTTGTAC
154884 TGTTTATATTATTTAAT
1 TGTTTATATTATTTAAT
154901 TGTTTA-ATTATATTAA
1 TGTTTATATTAT-TTAA
154917 ATTTGAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TGTTTATATTATTTAAT
Found at i:159763 original size:11 final size:10
Alignment explanation
Indices: 159747--159819 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 10
159737 CATCCACTTA
159747 ATAAAATATT
1 ATAAAATATT
159757 CATAAAA-ATT
1 -ATAAAATATT
159767 ATAAAATTATT
1 ATAAAA-TATT
*
159778 A-AAAAT-TA
1 ATAAAATATT
* *
159786 ATTAAA-ATC
1 ATAAAATATT
159795 ATAAAAGT-TT
1 ATAAAA-TATT
159805 ATAAAA-ATT
1 ATAAAATATT
159814 ATAAAA
1 ATAAAA
159820 AATCATAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
8 2 0.04
9 24 0.48
10 14 0.28
11 10 0.20
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (10 bp):
ATAAAATATT
Found at i:159791 original size:29 final size:29
Alignment explanation
Indices: 159759--159828 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
159749 AAAATATTCA
*
159759 TAAAAATTATAAAA--TTATTAAAAATTAAT
1 TAAAAATCATAAAAGTTTA-TAAAAATT-AT
159788 T-AAAATCATAAAAGTTTATAAAAATTAT
1 TAAAAATCATAAAAGTTTATAAAAATTAT
*
159816 AAAAAATCATAAA
1 TAAAAATCATAAA
159829 TTACATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 13 0.36
29 20 0.56
30 3 0.08
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (29 bp):
TAAAAATCATAAAAGTTTATAAAAATTAT
Found at i:159827 original size:19 final size:19
Alignment explanation
Indices: 159747--159828 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
159737 CATCCACTTA
159747 ATAAAATATTCAT-AAAAATT
1 ATAAAA-ATT-ATAAAAAATT
*
159767 AT-AAAATTATTAAAAATT
1 ATAAAAATTATAAAAAATT
* * **
159785 AATTAAAATCATAAAAGTTT
1 -ATAAAAATTATAAAAAATT
*
159805 ATAAAAATTATAAAAAATC
1 ATAAAAATTATAAAAAATT
159824 ATAAA
1 ATAAA
159829 TTACATATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
17 2 0.04
18 10 0.20
19 24 0.48
20 14 0.28
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (19 bp):
ATAAAAATTATAAAAAATT
Found at i:161431 original size:14 final size:15
Alignment explanation
Indices: 161407--161439 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
161397 GATGAGAATA
161407 AAAATTTAATTAAGT
1 AAAATTTAATTAAGT
*
161422 AAAA-TTAATTAATT
1 AAAATTTAATTAAGT
161436 AAAA
1 AAAA
161440 ATCTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AAAATTTAATTAAGT
Found at i:162143 original size:3 final size:3
Alignment explanation
Indices: 162135--162173 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
162125 CTCGTGAATT
162135 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
162174 CACAGATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:162464 original size:16 final size:18
Alignment explanation
Indices: 162425--162458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
162415 TAAGTTTATA
162425 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
162442 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
162459 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:168903 original size:28 final size:28
Alignment explanation
Indices: 168843--168903 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
168833 TTACATGGAC
*
168843 TGATTATTTAATTAATAAACGAAATACA
1 TGATTATTTAACTAATAAACGAAATACA
*
168871 AGATTATTTAACTACATAAAC-AATATA-A
1 TGATTATTTAACTA-ATAAACGAA-ATACA
168899 TGATT
1 TGATT
168904 TTACCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (28 bp):
TGATTATTTAACTAATAAACGAAATACA
Found at i:169135 original size:18 final size:18
Alignment explanation
Indices: 169099--169141 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
169089 TTAATTTTTT
* *
169099 ATTCGAATTAATTCGAATA
1 ATTCG-ATTAACTCAAATA
169118 ATTCGATTAACTCAAATA
1 ATTCGATTAACTCAAATA
*
169136 ACTCGA
1 ATTCGA
169142 ATTATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (18 bp):
ATTCGATTAACTCAAATA
Found at i:170187 original size:3 final size:3
Alignment explanation
Indices: 170179--170222 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
170169 CCAAAATCAA
* *
170179 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
170223 ATACTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:176489 original size:36 final size:36
Alignment explanation
Indices: 176442--176518 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
176432 GCTCTAACTT
176442 TCTGTCCAGCAGGGTAGTTCATCTCTATAAATAATC
1 TCTGTCCAGCAGGGTAGTTCATCTCTATAAATAATC
176478 TCTGTCCAGCAGGGTAGTTCATCTCTATAAATAATC
1 TCTGTCCAGCAGGGTAGTTCATCTCTATAAATAATC
176514 TCTGT
1 TCTGT
176519 AAATCCTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (36 bp):
TCTGTCCAGCAGGGTAGTTCATCTCTATAAATAATC
Found at i:181218 original size:21 final size:20
Alignment explanation
Indices: 181189--181229 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
181179 CAAATGTGTT
*
181189 AAAATTATTAATTTAAAATAA
1 AAAAATATT-ATTTAAAATAA
*
181210 AAAAATATTTTTTAAAATAA
1 AAAAATATTATTTAAAATAA
181230 TATAATTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATATTATTTAAAATAA
Found at i:200441 original size:2 final size:2
Alignment explanation
Indices: 200434--200458 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
200424 AGTTATTACT
200434 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
200459 TAGATAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:208090 original size:106 final size:106
Alignment explanation
Indices: 207900--208111 Score: 397
Period size: 106 Copynumber: 2.0 Consensus size: 106
207890 AATATGACAG
* *
207900 TGAAAGCAATGGTGGAGTACTTAGACGGATACACTAAGCTGAGTCGTTTCCATTCTTGATATGCT
1 TGAAAGCAATGGTGGAGTACTTAGAAGGATACACTAAGCTGAGTCGTTTCCATTCTTGATATGCC
207965 TTTGATAAATCATCAGGTTCATTAGATTTTCCACTTCTCTA
66 TTTGATAAATCATCAGGTTCATTAGATTTTCCACTTCTCTA
*
208006 TGAATGCAATGGTGGAGTACTTAGAAGGATACACTAAGCTGAGTCGTTTCCATTCTTGATATGCC
1 TGAAAGCAATGGTGGAGTACTTAGAAGGATACACTAAGCTGAGTCGTTTCCATTCTTGATATGCC
208071 TTTGATAAATCATCAGGTTCATTAGATTTTCCACTTCTCTA
66 TTTGATAAATCATCAGGTTCATTAGATTTTCCACTTCTCTA
208112 ACTTGTTTTC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (106 bp):
TGAAAGCAATGGTGGAGTACTTAGAAGGATACACTAAGCTGAGTCGTTTCCATTCTTGATATGCC
TTTGATAAATCATCAGGTTCATTAGATTTTCCACTTCTCTA
Found at i:211595 original size:18 final size:18
Alignment explanation
Indices: 211563--211614 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
211553 TTGAGATAAG
211563 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
211579 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
211597 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
211615 CAATTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:230480 original size:30 final size:30
Alignment explanation
Indices: 230444--230782 Score: 214
Period size: 30 Copynumber: 11.4 Consensus size: 30
230434 CGGAGAATAC
** *
230444 GAGGTCAAAACATAATTTTAGAAAAGTTTA
1 GAGGTCAAAATGTAATTTTGGAAAAGTTTA
*
230474 GAGGTCAAAATGTAATTTTGGAGAAGTTTA
1 GAGGTCAAAATGTAATTTTGGAAAAGTTTA
* * *
230504 -AGGGTCAAAATGCAATTTTGGAGAAGCTTA
1 GA-GGTCAAAATGTAATTTTGGAAAAGTTTA
* *
230534 G-TGTCAAAGCATG--ATTTTGGAAAGGTTTA
1 GAGGTCAAA--ATGTAATTTTGGAAAAGTTTA
* * *
230563 GGGGTCAAAGCATG--ATTTTGGAGAAGCTTAA
1 GAGGTCAAA--ATGTAATTTTGGAAAAG-TTTA
* *
230594 AAGGTCAAAATGTAATTTTGGAAAGGTTTA
1 GAGGTCAAAATGTAATTTTGGAAAAGTTTA
* * * * ***
230624 GGGGTTAAAATATGATTTTTTTTAAAGTTTA
1 GAGGTCAAAATGT-AATTTTGGAAAAGTTTA
* * *
230655 GGGGTTAAAATGTGATTTTGGAAAAGTTTA
1 GAGGTCAAAATGTAATTTTGGAAAAGTTTA
*
230685 G-GGTTAAAATGTAATTTTGGAAAAGTTTA
1 GAGGTCAAAATGTAATTTTGGAAAAGTTTA
* **
230714 -AGGGT-TAAATGTAATTTTATAAAAGTTT-
1 GA-GGTCAAAATGTAATTTTGGAAAAGTTTA
* * * *
230742 GAGGGT-TAAATGTAATATTAGATAAGTTTA
1 GA-GGTCAAAATGTAATTTTGGAAAAGTTTA
* *
230772 GGGGTTAAAAT
1 GAGGTCAAAAT
230783 ATGATTTTTA
Statistics
Matches: 252, Mismatches: 43, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
29 99 0.39
30 106 0.42
31 47 0.19
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
GAGGTCAAAATGTAATTTTGGAAAAGTTTA
Found at i:230689 original size:29 final size:29
Alignment explanation
Indices: 230456--230782 Score: 234
Period size: 29 Copynumber: 11.0 Consensus size: 29
230446 GGTCAAAACA
* *
230456 TAATTTTAGAAAAGTTTAGAGGTCAAAATG
1 TAATTTTGGAAAAGTTTAG-GGTTAAAATG
* *
230486 TAATTTTGGAGAAGTTTAAGGGTCAAAATG
1 TAATTTTGGAAAAGTTT-AGGGTTAAAATG
* * * * *
230516 CAATTTTGGAGAAGCTTAGTGTCAAAGCATG
1 TAATTTTGGAAAAGTTTAGGGTTAAA--ATG
* *
230547 --ATTTTGGAAAGGTTTAGGGGTCAAAGCATG
1 TAATTTTGGAAAAGTTTA-GGGTTAAA--ATG
* * * *
230577 --ATTTTGGAGAAGCTTAAAAGGTCAAAATG
1 TAATTTTGGAAAAG-TT-TAGGGTTAAAATG
* *
230606 TAATTTTGGAAAGGTTTAGGGGTTAAAATA
1 TAATTTTGGAAAAGTTTA-GGGTTAAAATG
* ***
230636 TGATTTTTTTTAAAGTTTAGGGGTTAAAATG
1 T-AATTTTGGAAAAGTTTA-GGGTTAAAATG
*
230667 TGATTTTGGAAAAGTTTAGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGTTAAAATG
230696 TAATTTTGGAAAAGTTTAAGGGTT-AAATG
1 TAATTTTGGAAAAGTTT-AGGGTTAAAATG
**
230725 TAATTTTATAAAAGTTTGAGGGTT-AAATG
1 TAATTTTGGAAAAGTTT-AGGGTTAAAATG
* * *
230754 TAATATTAGATAAGTTTAGGGGTTAAAAT
1 TAATTTTGGAAAAGTTTA-GGGTTAAAAT
230783 ATGATTTTTA
Statistics
Matches: 247, Mismatches: 37, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.00
29 102 0.41
30 95 0.38
31 48 0.19
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
TAATTTTGGAAAAGTTTAGGGTTAAAATG
Found at i:230739 original size:58 final size:58
Alignment explanation
Indices: 230456--230780 Score: 210
Period size: 59 Copynumber: 5.5 Consensus size: 58
230446 GGTCAAAACA
* * * *
230456 TAATTTTAGAAAAGTTTAGAGGTCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATG
1 TAATTTTAGAAAAGTTTAGGGGT-TAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATG
* * * * * * * * *
230516 CAATTTTGGAGAAGCTTA-GTGTCAAA-GCATGATTTTGGAAAGGTTTAGGGGTCAAAGCATG
1 TAATTTTAGAAAAGTTTAGGGGTTAAATG--TAATTTTGGAAAAGTTTA-GGGTTAAA--ATG
* * * ** * * *
230577 --ATTTTGGAGAAGCTTAAAAGGTCAAAATGTAATTTTGGAAAGGTTTAGGGGTTAAAATA
1 TAATTTTAGAAAAG-TTTAGGGGT-TAAATGTAATTTTGGAAAAGTTTA-GGGTTAAAATG
* *** *
230636 TGATTTTTTTTAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGTTAAAATG
1 T-AATTTTAGAAAAGTTTAGGGGTT-AAATGTAATTTTGGAAAAGTTTAGGGTTAAAATG
* * **
230696 TAATTTTGGAAAAGTTTAAGGGTTAAATGTAATTTTATAAAAGTTTGAGGGTT-AAATG
1 TAATTTTAGAAAAGTTTAGGGGTTAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATG
* *
230754 TAATATTAGATAAGTTTAGGGGTTAAA
1 TAATTTTAGAAAAGTTTAGGGGTTAAA
230781 ATATGATTTT
Statistics
Matches: 209, Mismatches: 42, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
57 1 0.00
58 51 0.24
59 62 0.30
60 27 0.13
61 57 0.27
62 10 0.05
63 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
TAATTTTAGAAAAGTTTAGGGGTTAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATG
Found at i:230798 original size:59 final size:59
Alignment explanation
Indices: 230647--230801 Score: 192
Period size: 58 Copynumber: 2.6 Consensus size: 59
230637 GATTTTTTTT
* * *
230647 AAAGTTTAGGGGTTAAAATGTGA-TTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTTAG-AAAGTTTAGGGTTAAAATGTAATATTAGA
* *
230706 AAAGTTTAAGGGTT-AAATGTAATTTTATA-AAAGTTTGAGGGTT-AAATGTAATATTAGA
1 AAAGTTTAGGGGTTAAAATGTGATTTT-TAGAAAGTTT-AGGGTTAAAATGTAATATTAGA
* *
230764 TAAGTTTAGGGGTTAAAATATGATTTTTAGAAAGTTTA
1 AAAGTTTAGGGGTTAAAATGTGATTTTTAGAAAGTTTA
230802 AGGACCATTA
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
58 42 0.51
59 39 0.48
60 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.39
Consensus pattern (59 bp):
AAAGTTTAGGGGTTAAAATGTGATTTTTAGAAAGTTTAGGGTTAAAATGTAATATTAGA
Found at i:234424 original size:16 final size:15
Alignment explanation
Indices: 234403--234432 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
234393 GTCAAAATTG
234403 TTAAAATTTATTTTTT
1 TTAAAATTT-TTTTTT
234419 TTAAAATTTTTTTT
1 TTAAAATTTTTTTT
234433 ATATTTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAAAATTTTTTTTT
Found at i:246974 original size:47 final size:47
Alignment explanation
Indices: 246922--247016 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
246912 AATCTGGAGG
246922 AGCATGTTGTCCATATAATAAATGCTCTTCTTTATTTCATAGTGCTA
1 AGCATGTTGTCCATATAATAAATGCTCTTCTTTATTTCATAGTGCTA
246969 AGCATGTTGTCCATATAATAAATGCTCTTCTTTATTTCATAGTGCTA
1 AGCATGTTGTCCATATAATAAATGCTCTTCTTTATTTCATAGTGCTA
247016 A
1 A
247017 CTCATTAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (47 bp):
AGCATGTTGTCCATATAATAAATGCTCTTCTTTATTTCATAGTGCTA
Found at i:250340 original size:16 final size:16
Alignment explanation
Indices: 250319--250371 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
250309 TTACTTCAAT
250319 AATAATATTCTAATGG
1 AATAATATTCTAATGG
**
250335 AATAATA-TGAAAT-G
1 AATAATATTCTAATGG
*
250349 AA-AATATTTTAATGG
1 AATAATATTCTAATGG
250364 AATAATAT
1 AATAATAT
250372 GAAATGAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 7 0.23
16 12 0.40
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (16 bp):
AATAATATTCTAATGG
Found at i:250364 original size:29 final size:29
Alignment explanation
Indices: 250322--250379 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
250312 CTTCAATAAT
250322 AATATTCTAATGGAATAATATGAAATGAA
1 AATATTCTAATGGAATAATATGAAATGAA
*
250351 AATATTTTAATGGAATAATATGAAATGAA
1 AATATTCTAATGGAATAATATGAAATGAA
250380 CCATAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.33
Consensus pattern (29 bp):
AATATTCTAATGGAATAATATGAAATGAA
Found at i:253428 original size:197 final size:197
Alignment explanation
Indices: 253090--253483 Score: 779
Period size: 197 Copynumber: 2.0 Consensus size: 197
253080 GTTAAGCAAG
253090 TAAATGGAGGCATAGTTTTGCTAACCATTAAATATAACATATATAGGCAATAGACAACTTAAAAT
1 TAAATGGAGGCATAGTTTTGCTAACCATTAAATATAACATATATAGGCAATAGACAACTTAAAAT
253155 TATCCAGCTAAAACTACGAAAATCATGCTAGGTATATAATGCACCAGCGTTGTTAGCACAAATTA
66 TATCCAGCTAAAACTACGAAAATCATGCTAGGTATATAATGCACCAGCGTTGTTAGCACAAATTA
253220 CATTCTATAGAGATTGTGTACAATCAAATTATTTCAAGAAATAGTATCGCAAACTTCGGGCTGCA
131 CATTCTATAGAGATTGTGTACAATCAAATTATTTCAAGAAATAGTATCGCAAACTTCGGGCTGCA
253285 CA
196 CA
253287 TAAATGGAGGCATAGTTTTGCTAACCATTAAATATAACATATATAGGCAATAGACAACTTAAAAT
1 TAAATGGAGGCATAGTTTTGCTAACCATTAAATATAACATATATAGGCAATAGACAACTTAAAAT
253352 TATCCAGCTAAAACTACGAAAATCATGCTAGGTATATAATGCACCAGCGTTGTTAGCACAAATTA
66 TATCCAGCTAAAACTACGAAAATCATGCTAGGTATATAATGCACCAGCGTTGTTAGCACAAATTA
*
253417 CATTTTATAGAGATTGTGTACAATCAAATTATTTCAAGAAATAGTATCGCAAACTTCGGGCTGCA
131 CATTCTATAGAGATTGTGTACAATCAAATTATTTCAAGAAATAGTATCGCAAACTTCGGGCTGCA
253482 CA
196 CA
253484 CATGTGATAC
Statistics
Matches: 196, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
197 196 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (197 bp):
TAAATGGAGGCATAGTTTTGCTAACCATTAAATATAACATATATAGGCAATAGACAACTTAAAAT
TATCCAGCTAAAACTACGAAAATCATGCTAGGTATATAATGCACCAGCGTTGTTAGCACAAATTA
CATTCTATAGAGATTGTGTACAATCAAATTATTTCAAGAAATAGTATCGCAAACTTCGGGCTGCA
CA
Found at i:254974 original size:10 final size:9
Alignment explanation
Indices: 254938--254973 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
254928 TTTAACTATC
254938 ATTTTCTTG
1 ATTTTCTTG
254947 ATTTTCTTG
1 ATTTTCTTG
*
254956 ATTTTCTTT
1 ATTTTCTTG
254965 ATTATTCTT
1 ATT-TTCTT
254974 TTTCTAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.14, C:0.11, G:0.06, T:0.69
Consensus pattern (9 bp):
ATTTTCTTG
Found at i:266984 original size:18 final size:18
Alignment explanation
Indices: 266963--267001 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
266953 TTATAATATA
266963 ATAAT-ATTATTTAATTTT
1 ATAATCATTA-TTAATTTT
*
266981 ATAATCATTATTATTTTT
1 ATAATCATTATTAATTTT
266999 ATA
1 ATA
267002 CTAATCGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAATCATTATTAATTTT
Found at i:268522 original size:16 final size:16
Alignment explanation
Indices: 268498--268545 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
268488 AATTAAATAA
268498 AAATAATATAAAATTT
1 AAATAATATAAAATTT
**
268514 ATAAT-ATATAATCTTT
1 A-AATAATATAAAATTT
268530 AAATAATATAAAATTT
1 AAATAATATAAAATTT
268546 CTATAACACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAATATAAAATTT
Found at i:268551 original size:16 final size:15
Alignment explanation
Indices: 268500--268551 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 15
268490 TTAAATAAAA
268500 ATAATATAAAA-TTT
1 ATAATATAAAATTTT
*
268514 ATAATATATAATCTTT
1 ATAATATAAAAT-TTT
268530 AAATAATATAAAATTTCT
1 --ATAATATAAAATTT-T
268548 ATAA
1 ATAA
268552 CACTTCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 10 0.32
16 7 0.23
17 2 0.06
18 12 0.39
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATAAAATTTT
Found at i:268565 original size:32 final size:32
Alignment explanation
Indices: 268498--268571 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
268488 AATTAAATAA
*
268498 AAATAATATAAAATTTATAATATATAATCTTT
1 AAATAATATAAAATTTATAATATACAATCTTT
* *
268530 AAATAATATAAAATTTCT-ATA-ACACTTCTTAT
1 AAATAATATAAAATTTATAATATACA-ATCTT-T
268562 AAATAATATA
1 AAATAATATA
268572 TTTTTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.05
31 7 0.19
32 28 0.76
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (32 bp):
AAATAATATAAAATTTATAATATACAATCTTT
Found at i:269631 original size:26 final size:27
Alignment explanation
Indices: 269583--269638 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
269573 GAACATTTAT
**
269583 TATTAATATTTTATAATTATAATAA-A
1 TATTAATATTGAATAATTATAATAATA
* *
269609 TATTAATATTGAATATTTTTAATAATA
1 TATTAATATTGAATAATTATAATAATA
269636 TAT
1 TAT
269639 GAAGAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTAATATTGAATAATTATAATAATA
Found at i:271214 original size:16 final size:17
Alignment explanation
Indices: 271182--271216 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
271172 AATACTTACA
*
271182 AATTGTGTTTATAATTT
1 AATTGCGTTTATAATTT
271199 AATTGCGTTT-TAATTT
1 AATTGCGTTTATAATTT
271215 AA
1 AA
271217 ATATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (17 bp):
AATTGCGTTTATAATTT
Found at i:272657 original size:213 final size:213
Alignment explanation
Indices: 272283--272920 Score: 1249
Period size: 213 Copynumber: 3.0 Consensus size: 213
272273 AGGCAAACAA
* *
272283 AAGTGACTATTTTTATTGTTTACCCTTATGTTAATTGATAATAACGTAATATACTATTACCTATT
1 AAGTGATTATTTTTATTGTTTACCCTTATATTAATTGATAATAACGTAATATACTATTACCTATT
272348 TTTTATTATTTCAATTTAATATTGTAGTTTTTCTTATATATTTGATTTAAATTATTTTAGGGAAT
66 TTTTATTATTTCAATTTAATATTGTAGTTTTTCTTATATATTTGATTTAAATTATTTTAGGGAAT
272413 TAAAATTTAAGCATTGATATTTTTTTAAGGTTAGTAAGAGTTTTGATTGTGTTGCAAAATCGATT
131 TAAAATTTAAGCATTGATATTTTTTTAAGGTTAGTAAGAGTTTTGATTGTGTTGCAAAATCGATT
272478 CCCTTTTTCGAAGGCATG
196 CCCTTTTTCGAAGGCATG
272496 AAGTGATTATTTTTATTGTTTACCCTTATATTAATTGATAATAACGTAATATACTATTACCTATT
1 AAGTGATTATTTTTATTGTTTACCCTTATATTAATTGATAATAACGTAATATACTATTACCTATT
272561 TTTTATTATTTCAATTTAATATTGTAGTTTTTCTTATATATTTGATTTAAATTATTTTAGGGAAT
66 TTTTATTATTTCAATTTAATATTGTAGTTTTTCTTATATATTTGATTTAAATTATTTTAGGGAAT
272626 TAAAATTTAAGCATTGATATTTTTTTAAGGTTAGTAAGAGTTTTGATTGTGTTGCAAAATCGATT
131 TAAAATTTAAGCATTGATATTTTTTTAAGGTTAGTAAGAGTTTTGATTGTGTTGCAAAATCGATT
272691 CCCTTTTTCGAAGGCATG
196 CCCTTTTTCGAAGGCATG
272709 AAGTGATTATTTTTATTGTTTACCCTTATATTAATTGATAATAACGTAATATACTATTACCTATT
1 AAGTGATTATTTTTATTGTTTACCCTTATATTAATTGATAATAACGTAATATACTATTACCTATT
272774 TTTTATTATTTCAATTTAATATTGTAGTTTTTCTTATATATTTGATTTAAATTATTTTAGGGAAT
66 TTTTATTATTTCAATTTAATATTGTAGTTTTTCTTATATATTTGATTTAAATTATTTTAGGGAAT
*
272839 TAAAATTTAAGCATTGATATTTTTTTAAGGTTAGTAAGAGTTTTGATTGTGTTGCAAAATCGAAT
131 TAAAATTTAAGCATTGATATTTTTTTAAGGTTAGTAAGAGTTTTGATTGTGTTGCAAAATCGATT
272904 CCCTTTTTCGAAGGCAT
196 CCCTTTTTCGAAGGCAT
272921 TATGTGATGA
Statistics
Matches: 422, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 422 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.49
Consensus pattern (213 bp):
AAGTGATTATTTTTATTGTTTACCCTTATATTAATTGATAATAACGTAATATACTATTACCTATT
TTTTATTATTTCAATTTAATATTGTAGTTTTTCTTATATATTTGATTTAAATTATTTTAGGGAAT
TAAAATTTAAGCATTGATATTTTTTTAAGGTTAGTAAGAGTTTTGATTGTGTTGCAAAATCGATT
CCCTTTTTCGAAGGCATG
Found at i:273004 original size:15 final size:15
Alignment explanation
Indices: 272986--273056 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
272976 TATTATCATA
*
272986 AATATATTATTATTT
1 AATATATTATAATTT
**
273001 AATATAAAATAATTT
1 AATATATTATAATTT
*
273016 AAATATAATTTATTATTT
1 -AATAT-A-TTATAATTT
*
273034 AATATGAGTATAATTT
1 AATAT-ATTATAATTT
273050 AA-ATATT
1 AATATATT
273057 TAAAAAATAG
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
14 2 0.05
15 14 0.33
16 14 0.33
17 7 0.16
18 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
AATATATTATAATTT
Found at i:273034 original size:33 final size:32
Alignment explanation
Indices: 272984--273055 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
272974 TTTATTATCA
272984 TAAATATATTATTATTTAATAT-AAAATAATT
1 TAAATATATTATTATTTAATATGAAAATAATT
**
273015 TAAATATAATTTATTATTTAATATGAGTATAATT
1 TAAATAT-A-TTATTATTTAATATGAAAATAATT
273049 TAAATAT
1 TAAATAT
273056 TTAAAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 7 0.19
32 1 0.03
33 14 0.39
34 14 0.39
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
TAAATATATTATTATTTAATATGAAAATAATT
Found at i:275260 original size:16 final size:17
Alignment explanation
Indices: 275239--275273 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
275229 TATAAATTGT
*
275239 ATTATATTAT-AACATA
1 ATTATATGATAAACATA
275255 ATTATATGATAAACATA
1 ATTATATGATAAACATA
275272 AT
1 AT
275274 GTATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (17 bp):
ATTATATGATAAACATA
Found at i:276133 original size:18 final size:19
Alignment explanation
Indices: 276103--276142 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
276093 TAATAAGCAA
276103 TTATACTTTTATTA-TTAT
1 TTATACTTTTATTATTTAT
276121 TTAT-CTTTGTATTATTTAT
1 TTATACTTT-TATTATTTAT
276140 TTA
1 TTA
276143 GTGTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATACTTTTATTATTTAT
Found at i:279629 original size:27 final size:24
Alignment explanation
Indices: 279571--279627 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
279561 TTAGCTGTGA
279571 CAGATGATGGTACTACAATAGTTC
1 CAGATGATGGTACTACAATAGTTC
279595 CAGATGATGGTACTACAATAGTTC
1 CAGATGATGGTACTACAATAGTTC
279619 CAGATGATG
1 CAGATGATG
279628 ATCCCAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (24 bp):
CAGATGATGGTACTACAATAGTTC
Found at i:287798 original size:4 final size:4
Alignment explanation
Indices: 287784--287842 Score: 64
Period size: 4 Copynumber: 14.2 Consensus size: 4
287774 AAAATTGAAG
* * * *
287784 GAAA AAAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAAG GAAG
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
287833 GAGAA GAAA G
1 GA-AA GAAA G
287843 GGAAAAAGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
4 41 0.87
5 6 0.13
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:287839 original size:25 final size:25
Alignment explanation
Indices: 287780--287860 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
287770 AACGAAAATT
*
287780 GAAGGAAAAAAAGAAAGAAAAAAGA
1 GAAGGAAAGAAAGAAAGAAAAAAGA
* *
287805 GAAAGAAAGAAAGAAAGAAAGAAG-
1 GAAGGAAAGAAAGAAAGAAAAAAGA
* *
287829 GAAGGAGAAGAAAG--GGAAAAAGGA
1 GAAGGA-AAGAAAGAAAGAAAAAAGA
287853 GAAGGAAA
1 GAAGGAAA
287861 TAAAAGATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 8 0.17
24 11 0.23
25 28 0.60
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
GAAGGAAAGAAAGAAAGAAAAAAGA
Found at i:288052 original size:12 final size:12
Alignment explanation
Indices: 288035--288059 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
288025 TTAAGTACGG
288035 TTAATTTTAAAA
1 TTAATTTTAAAA
288047 TTAATTTTAAAA
1 TTAATTTTAAAA
288059 T
1 T
288060 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:288258 original size:20 final size:21
Alignment explanation
Indices: 288217--288261 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
288207 TAATTTACTT
288217 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
288238 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
288258 TAAT
1 TAAT
288262 AGTAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.